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Chthonobacter rhizosphaerae sp. nov., a bacterium isolated from rhizosphere soil of Citrus sinenesis

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Abstract

A Gram-staining negative, facultative anaerobic, motile and short rod-shaped bacterium, designated strain yh7-1T, was isolated from rhizosphere soil of Citrus sinenesis collected from the garden of Citrus sinenesis in Ailao Mountain, south-west China. Cells grew at 15–45 °C, pH 5.0–9.0 and were able to tolerate up to 1% (w/v) NaCl on R2A medium. The respiratory lipoquinone was Q-10 and the major cellular fatty acids contained summed feature 8 (C18:1 ω7c or C18:1 ω6c) and C18:0. Polar lipids in the cellular membrane were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and one unidentified aminophospholipid. The genomic DNA G+C content was 69.9 mol%. On basis of 16S rRNA gene sequence analysis, strain yh7-1T showed the highest similarities with Chthonobacter albigriseus KCTC 42450T (97.6%), Mongoliimonas terrestris KCTC 42635T (97.0%) and lower than 97.0% to other species. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain yh7-1T clustered with C. albigriseus KCTC 42450T. The ANI values ranged between 78.1 and 82.7% for C. albigriseus KCTC 42450T, M. terrestris KCTC 42635T and strain yh7-1T, which were lower than the prokaryotic species delineation threshold of 95.0–96.0%. The digital DNA–DNA hybridization values between C. albigriseus KCTC 42450T, M. terrestris KCTC 42635T and strain yh7-1T indicated that the new isolate represents a novel genomic species. According to the phenotypic and genotypic characteristics, strain yh7-1T should belong to the genus Chthonobacter, for which the name Chthonobacter rhizosphaerae sp. nov. (type strain yh7-1T = CGMCC 1.17236T = CCTCC AB 2019258T = KCTC 82185T) is proposed.

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Data availability

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain yh7-1T is MG209703. The whole Genomes shotgun project of strain yh7-1T and Mongoliimonas terrestris KCTC 42635T have been deposited at DDBJ/ENA/GenBank under the accession numbers JACDIS000000000 and JACDIT000000000, respectively.

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Acknowledgements

The authors are grateful to Professor Jung-Sook Lee (KCTC, Korea) for kindly providing the reference type strain. This research was supported by the Foundation of China Tobacco Yunnan Industrial Co., Ltd. (2020CL04 and 2018CP04).

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Author notes

  1. Xiu-Ming Liu and Xing-Kui Zhou contributed equally to this work.

Authors and Affiliations

  1. China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People’s Republic of China

    Xiu-Ming Liu, Xing-Kui Zhou, Yuan-Dong Li, Ju-Xing Jiang, Li-Min Dong & Yan-Qing Duan

  2. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, People’s Republic of China

    Xing-Kui Zhou

  3. State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Bao-Zhu Fang & Wen-Jun Li

  4. State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Urumqi, 830011, People’s Republic of China

    Bao-Zhu Fang & Wen-Jun Li

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  1. Xiu-Ming Liu
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Contributions

YQD and WJL designed research and project outline. XML, ZXK, LMD performed isolation, deposition, and identification. ZXK, YDL BZF and JXJ performed fatty acids analysis. All authors read and approved the final manuscript.

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Correspondence to Wen-Jun Li or Yan-Qing Duan.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Communicated by Erko Stackebrandt.

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Liu, XM., Zhou, XK., Li, YD. et al. Chthonobacter rhizosphaerae sp. nov., a bacterium isolated from rhizosphere soil of Citrus sinenesis. Arch Microbiol 203, 2343–2350 (2021). https://doi.org/10.1007/s00203-021-02217-6

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